Sounds like you hit the nail though... character "development" and deep long-lasting choices that impact you are pretty hard to pull of in a co-op experience. It's rather hard to have super long conversations with teammate with permanent results if that leads to the other player just waiting. Or if you want to give them input, the same happens; you need to give both players a choice, and that may lead to back-and-forth.
Not to say I'm not much a fan of the RPS minigame myself, and would see a less intrucive system in the sequel (like just a roll with modifiers depending on your skills, and maybe add a little bonus each time a player fails till they succeed so it's very unlikely it's a one-man-show).
